Also: what if some app/service recognizes a jailbroken iPhone as being "bad" at some point in its life, saving the "bad flag" in some database, leaving a black mark on the warranty record? Feasible? Any known app/service/mechanism that does this? (Maybe Apple wouldn't care so long as you reinstall, hence no motivation for such a thing?)
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Johnny UtahhMar 26 '12 at 23:50

5 Answers
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JailBreaking only affects the software, and restoring a JailBroken device to an official version of the iOS firmware will essentially make your phone "not JailBroken." Restoring the device simply means reinstalling iOS normally through iTunes by either selecting the "Update" or "Restore" button, and can be done to any device regardless of whether or not they are currently or have previously been JailBroken.

However, there have been a few cases where I have run into issues that made my device temporarily unusable (I honestly thought I had bricked my iPod). There was a slight difference in the way iOS 4.3.3 was exploited, and it made it difficult to restore. When you went into iTunes to restore, it would return you errors 1394, 2005, or 1601 (or a plethora of others) during the verification process (this is where iTunes checks with Apple to make sure you're using an official .ipsw (the actual firmware package)). It didn't matter if you were using a modified .ipsw or an official one, it would always fail. There were a few things that you had to try to fix it, and if you didn't do it right, you ended up with a different error code that you've never seen before. You had to either modify your hosts file (it associates IP addresses with domain names, so that iTunes was going to the right place to verify the install), put your device in "Pwned DFU" mode (it's a half-JailBroken state that doesn't require you to use an official .ipsw inside of iTunes) with iREB, or use redsn0w to install iOS for you. After having no luck with the other solutions, I ended up having to download the official iOS 5.0.1 firmware from Apple and then installing it with redsn0w. For the most part, redsn0w is for installing modified firmwares or for JailBreaking existing ones, but in this case, I had to use it to merely bypass iTunes's verification.

In conclusion, most devices will just be an easy one-click install for restoring iOS. Apple cannot tell if you've previously been JailBroken if you do a full restore. Doing a full restore means that you set it back to factory defaults. It erases everything including data in your /private/var/mobile/ profile. A standard update will not delete data here, because iTunes backs up your profile before it installs and then loads it back on when it's finished. Some JailBreak tweaks store their preferences in .plist files in /private/var/mobile/Library/Preferences/, so if Apple really wanted to see if you've been JailBroken before, they could check there for any files from unapproved apps/tweaks (so make sure you erase everyhing if you're worried about Apple knowing you JailBroke it). A full restore is done best with redsn0w, because I've had times where iTunes uses my backup data even when I clicked the "Restore" button.

There aren't any apps that I know of that leave a "mark" like you mentioned in a comment. There are some apps like Skype that yell at you if you're JailBroken, but the app still works. If you're still worried, a full restore would get rid of anything and everything on the device.

For the most part, and if you do it correctly, Apple cannot tell if your device has ever been JailBroken, so you'll be "supported by Apple" again.

Fwiw. Spoke with an Apple rep at a retail, brick-and-mortar (sort of) Apple Store today. Rep said that he actually worked to confirm a customer's iPhone hardware prob by reinstalling iOS on customer's jailbroken phone, and that it was "totally cool" by him, no known (or at least strict) Apple policy against such a thing.

To avoid trouble and if you want to make sure all residual files are removed I would recommend restoring in DFU mode using the latest iOS firmware and setup the device as a new iPhone after the restore.

I had to use jailbroken iPhones for testing and this worked for me, no application ever complained that the phones are jailbroken after a full restore.

Thx. You write "restoring the iPhone..." Does "restoration" involve anything other than an iOS reinstall? And can said iOS reinstall work for any jailbroken iPhone?
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Johnny UtahhMar 26 '12 at 15:03

Could you please and some substantial confirmation to your answer. Is this something the developers of the jailbreak say? I'd really like to believe this answer. But for now it seems insufficient ;)
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gentmattMar 26 '12 at 15:04

@gentmatt It worked for me, I needed jailbroken iPhones to use on an unsupported carrier for testing. Restoring them afterwards did bring them "back" to a non jailbroken state although with a newer firmware. I don't know about any official statements from the jail breaking community, but the hardware team at my employer was positive about restoring to bring the device back to normal.
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CoyoteMar 26 '12 at 15:27

Thx. Does anyone know if an iOS reinstall would ever fail (say because of jailbreaking or any other reason, weird scenario) on working iPhone hardware? ie, is the iOS reinstall/restore "bullet proof," similar to how an Linux/Windows/MacOS reinstall works on my any desktop/laptop (that was previously and successfully running the re-installing OS)?
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Johnny UtahhMar 26 '12 at 16:29

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@JohnnyUtahh I don't think this is relevant to the original question, but to answer your latest question my understanding is that some unofficial firmwares modify the baseband (for SIM unlock) which then can lead to added difficulty when restoring. Restoring in DFU mode should fix the problem. If not you will have to use an alternative firmware loader in place of iTunes to force the restoration.
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CoyoteMar 26 '12 at 19:41

Ostensibly there is no difference between a brand new phone running 5.1, and one that was jailbroken, and then restored via a full reinstall to the same OS Level. It should not leave any traces of it's history in there, so long as you set it up as a new iphone in iTunes, and do not subsequently throw a restore over the top which could reasonably be expected to hold old data etc.